petab.measurements
Functions operating on the PEtab measurement table
Functions
Ensure that number of parameters in the observable definition matches the number of overrides in |
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Create empty measurement dataframe |
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Read the provided measurement file into a |
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Return list of ID of parameters which occur in measurement table as observable or noise parameter overrides. |
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Extract rows in measurement_df for condition according to 'preequilibrationConditionId' and 'simulationConditionId' in condition. |
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Create a table of separate simulation conditions. |
Check whether a measurement is at steady state. |
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Tests whether the measurements come with replicates |
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Split values in observableParameters and noiseParameters in measurement table. |
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Write PEtab measurement table |
- petab.measurements.assert_overrides_match_parameter_count(measurement_df: DataFrame, observable_df: DataFrame) None [source]
Ensure that number of parameters in the observable definition matches the number of overrides in
measurement_df
- Parameters
measurement_df – PEtab measurement table
observable_df – PEtab observable table
- petab.measurements.create_measurement_df() DataFrame [source]
Create empty measurement dataframe
- Returns
Created DataFrame
- petab.measurements.get_measurement_df(measurement_file: Union[None, str, Path, DataFrame]) DataFrame [source]
Read the provided measurement file into a
pandas.Dataframe
.- Parameters
measurement_file – Name of file to read from or pandas.Dataframe
- Returns
Measurement DataFrame
- petab.measurements.get_measurement_parameter_ids(measurement_df: DataFrame) List[str] [source]
Return list of ID of parameters which occur in measurement table as observable or noise parameter overrides.
- Parameters
measurement_df – PEtab measurement DataFrame
- Returns
List of parameter IDs
- petab.measurements.get_rows_for_condition(measurement_df: DataFrame, condition: Union[Series, DataFrame, Dict]) DataFrame [source]
Extract rows in measurement_df for condition according to ‘preequilibrationConditionId’ and ‘simulationConditionId’ in condition.
- Parameters
measurement_df – PEtab measurement DataFrame
condition – DataFrame with single row (or Series) and columns ‘preequilibrationConditionId’ and ‘simulationConditionId’. Or dictionary with those keys.
- Returns
The subselection of rows in
measurement_df
for the conditioncondition
.
- petab.measurements.get_simulation_conditions(measurement_df: DataFrame) DataFrame [source]
Create a table of separate simulation conditions. A simulation condition is a specific combination of simulationConditionId and preequilibrationConditionId.
- Parameters
measurement_df – PEtab measurement table
- Returns
Dataframe with columns ‘simulationConditionId’ and ‘preequilibrationConditionId’. All-null columns will be omitted. Missing ‘preequilibrationConditionId’s will be set to ‘’ (empty string).
- petab.measurements.measurement_is_at_steady_state(time: float) bool [source]
Check whether a measurement is at steady state.
- Parameters
time – The time.
- Returns
Whether the measurement is at steady state.
- petab.measurements.measurements_have_replicates(measurement_df: DataFrame) bool [source]
Tests whether the measurements come with replicates
- Parameters
measurement_df – Measurement table
- Returns
True
if there are replicates,False
otherwise
- petab.measurements.split_parameter_replacement_list(list_string: Union[str, Number], delim: str = ';') List[Union[str, Number]] [source]
Split values in observableParameters and noiseParameters in measurement table.
- Parameters
list_string – delim-separated stringified list
delim – delimiter
- Returns
List of split values. Numeric values may be converted to float, and parameter IDs are kept as strings.